knitr::opts_chunk$set( echo = TRUE, collapse = TRUE, comment = "#>", fig.path = "man/figures/README-", out.width = "100%" )
tidysq
contains tools for analysis and manipulation of biological sequences (including amino acid and nucleic acid -- e.g. RNA, DNA -- sequences). Two major features of this package are:
effective compression of sequence data, allowing to fit larger datasets in R,
compatibility with most of tidyverse
universe, especially dplyr
and vctrs
packages, making analyses tidier.
Try our quick start vignette or our exhaustive documentation.
The easiest way to install tidysq
package is to download its latest version from CRAN repository:
install.packages("tidysq")
Alternatively, it is possible to download the development version directly from GitHub repository:
# install.packages("devtools") devtools::install_github("BioGenies/tidysq")
library(tidysq)
file <- system.file("examples", "example_aa.fasta", package = "tidysq") sqibble <- read_fasta(file) sqibble sq_ami <- sqibble$sq sq_ami # Subsequences can be extracted with bite() bite(sq_ami, 5:10) # There are also more traditional functions reverse(sq_ami) # find_motifs() returns a whole tibble of useful informations find_motifs(sqibble, "^VHX")
An example of dplyr
integration:
library(dplyr) # tidysq integrates well with dplyr verbs sqibble %>% filter(sq %has% "VFF") %>% mutate(length = get_sq_lengths(sq))
For citation type:
citation("tidysq")
or use:
Michal Burdukiewicz, Dominik Rafacz, Laura Bakala, Jadwiga Slowik, Weronika Puchala, Filip Pietluch, Katarzyna Sidorczuk, Stefan Roediger and Leon Eyrich Jessen (2021). tidysq: Tidy Processing and Analysis of Biological Sequences. R package version 1.1.3.
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